Contacts of the strand formed by residues 106 - 113 (chain D) in PDB entry 3AQQ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLU 106 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63B TYR* 4.0 1.4 - - - -
83B ASP* 2.4 35.3 - - - +
64D LYS* 3.0 35.5 + - + +
65D GLY 3.3 15.9 - - - +
66D VAL* 4.5 10.3 - - + +
104D GLY 3.3 5.0 + - - +
105D ASP* 1.3 70.5 - - - +
107D VAL* 1.3 63.8 + - - +
128D ILE* 3.5 2.1 - - - -
129D THR* 2.8 30.1 + - - +
130D HIS* 2.8 45.7 + - + +
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Residues in contact with VAL 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D LYS* 3.3 5.1 - - - +
65D GLY* 2.7 57.8 + - - +
66D VAL* 3.9 3.8 - - - +
67D CYS* 4.4 6.1 - - + +
79D ILE* 3.8 27.4 - - + -
101D PRO* 6.2 1.6 - - + -
105D ASP* 3.9 13.5 - - + +
106D GLU* 1.3 80.9 - - - +
108D THR* 1.3 66.5 + - - +
109D TYR* 3.9 6.2 - - + -
126D VAL* 4.4 9.9 - - + -
127D VAL 3.0 15.0 - - - +
128D ILE* 4.0 16.2 - - + -
129D THR* 4.2 2.5 - - - +
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Residues in contact with THR 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B PRO* 3.7 21.1 - - + -
63B TYR* 3.0 28.5 - - - +
58C SER* 4.2 6.8 + - - -
59C GLN* 4.9 7.6 + - - +
62D VAL* 3.9 11.4 - - + -
63D TYR 3.1 5.6 - - - +
64D LYS* 4.7 1.1 - - + -
107D VAL* 1.3 76.2 - - - +
109D TYR* 1.3 64.8 + - - +
125D GLU 4.3 0.9 - - - -
126D VAL* 3.5 1.9 - - - +
127D VAL* 2.9 51.0 + - - +
129D THR* 3.4 11.7 - - + +
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Residues in contact with TYR 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D VAL* 3.7 4.1 - - - +
63D TYR* 2.9 48.7 + - + +
64D LYS 3.3 30.7 + - - -
65D GLY 3.9 1.1 - - - -
79D ILE* 4.0 17.9 - - + -
81D PRO* 3.8 17.8 - - - +
88D ILE* 4.2 8.6 - - + +
107D VAL* 3.9 12.3 - - + -
108D THR* 1.3 81.7 - - - +
110D LYS* 1.3 75.1 + - - +
111D MET* 3.7 36.8 - - + +
123D ALA* 3.9 12.3 - - + -
124D VAL 3.7 8.5 - - - +
125D GLU 3.6 9.2 - - - -
126D VAL* 3.9 15.9 - - + -
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Residues in contact with LYS 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C LYS* 4.2 15.6 - - - +
125C GLU* 4.6 0.6 + - - -
57D ALA 3.2 26.2 - - - +
58D SER* 3.2 28.3 - - - +
60D GLY 4.2 7.2 - - - +
61D PRO 3.8 15.3 - - - +
62D VAL* 4.3 19.4 - - + +
109D TYR* 1.3 85.5 - - - +
111D MET* 1.3 62.4 + - - +
123D ALA* 3.5 0.2 - - - -
124D VAL* 2.9 41.4 + - + +
125D GLU* 2.9 32.7 + - + +
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Residues in contact with MET 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D ALA* 3.5 24.3 + - - +
61D PRO* 4.5 4.4 + - - +
63D TYR* 4.0 29.1 - - + -
81D PRO* 5.1 5.6 - - + -
83D ASP* 5.8 2.5 - - - +
88D ILE* 3.6 25.8 - - + -
109D TYR* 3.7 35.4 - - + +
110D LYS* 1.3 74.8 - - - +
112D CYS* 1.3 63.4 + - - +
121D LEU* 3.1 32.1 - - + -
122D GLN 3.4 10.1 - - - +
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Residues in contact with CYS 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D ARG* 3.7 32.1 - - - -
53D ALA* 4.4 13.2 - - - -
57D ALA* 4.0 13.2 - - - +
111D MET* 1.3 77.2 - - - +
113D SER* 1.3 67.7 + - - +
121D LEU* 3.2 10.1 - - - +
122D GLN* 2.6 46.5 + - + +
124D VAL* 3.7 18.2 - - + -
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Residues in contact with SER 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D ALA* 5.6 2.9 - - - +
56D ARG* 6.1 2.5 - - - -
112D CYS* 1.3 85.5 - - - +
114D ILE* 1.3 60.8 + - - +
115D PRO* 3.4 11.6 - - - +
118D ASN* 3.1 35.7 - - - +
119D GLU 3.7 5.2 + - - -
120D LYS 3.1 17.2 + - - -
121D LEU* 3.8 8.4 - - - +
122D GLN* 5.3 1.2 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il